Four-Way Junction-Driven DNA Strand Displacement and Its Application in Building Majority Logic Circuit

We introduced a four-way DNA junction-driven toehold-mediated strand displacement method. Separation of the different functional domains on different strands in the four-way junction structure and usage of glue strand to recombine them for different logic gates make the design more flexible. On the basis of this mechanism, a majority logic circuit fabricated by DNA strands was designed and constructed by assembling three AND gates and one OR gate together. The output strand drew the G-rich segments together to form a split G-quadruplex, which could specifically bind PPIX and enhance its fluorescence. Just like a poll with three voters, the high fluorescence signal would be given off only when two or three voters vote in favor. Upon slight modification, the majority circuit was utilized to select the composite number from 0 to 9 represented by excess-three code. It is a successful attempt to integrate the logic gates into a circuit and to achieve desired functions

Bifunctional Colorimetric Oligonucleotide Probe Based on a G-Quadruplex DNAzyme Molecular Beacon

A label-free bifunctional colorimetric oligonucleotide probe for DNA and protein detection has been developed on the basis of a novel catalytic molecular beacon consisting of two hairpin structures and a split G-quadruplex DNAzyme in the middle. The two loops of this molecular beacon consist of thrombin aptamer sequence and the complementary sequence of target DNA, which are utilized to sense single-stranded DNA and thrombin. The G-quadruplex DNAzyme can effectively catalyze the H₂O₂-mediated oxidation of 3,3′,5,5′-tetramethylbenzidine sulfate to generate colorimetric signal. Upon addition of the target, the DNA or protein combines with one loop of the hairpin structures, and meanwhile drives the middle G-quadruplex DNAzyme to dissociate. This results in a decrease of catalytic activity, enabling the separate analysis of DNA and thrombin

Pd Nanowires as New Biosensing Materials for Magnified Fluorescent Detection of Nucleic Acid

The designed synthesis of new nanomaterials with controlled shape, composition, and structure is critical for tuning their physical and chemical properties, and further developing interesting analytical sensing devices. Herein, we presented that Pd nanowires (NWs) can be used as a new biosensing platform for high-sensitivity nucleic acid detection. The general sensing concept is based on the fact that Pd NWs can adsorb the fluorescently labeled single-stranded DNA probe and lead to substantial fluorescence quenching of dye, followed by specific hybridization with the complementary region of the target DNA sequence. This results in desorption of double-stranded DNA from Pd NWs surface and subsequent recovery of fluorescence. Furthermore, an amplification strategy based on Pd NWs for nucleic acid detection by using exonuclease III (Exo III) was demonstrated. The present dual-magnification sensing system combined Pd NWs with Exo III has a detection range of 1.0 nM to 2.0 μM with the detection limit of 0.3 nM (S/N = 3), which is about 20-fold higher than that of traditional unamplified homogeneous assays

New Insight into a Microfluidic-Based Bipolar System for an Electrochemiluminescence Sensing Platform

In this work, a novel style of a microfluidic-based bipolar system with two-direction driving electrodes and dual-channel configuration was described for the first time, which could reach 100% current efficiency in theory. More importantly, the background signal from the integrated driving electrodes was completely eliminated, when this unique design was used to construct an electrochemiluminescence (ECL) sensing platform. First, universal pH indicator was employed to study the mechanism and demonstrate that this new bipolar system possessed 100% current efficiency theoretically. Then, the Ru­(bpy)₃²⁺/TPrA ECL system was introduced to construct the dual-channel bipolar ECL sensing platform, and the results of visual ECL experiments proved that the background signals from the driving electrodes were completely dispelled with our design. To illustrate the promising applications of this dual-channel device, TPrA, dopamine (DA), H₂O₂, and K₃Fe­(CN)₆ were detected as model targets under different principles

Aptamer-Based Sensing Platform Using Three-Way DNA Junction-Driven Strand Displacement and Its Application in DNA Logic Circuit

We proposed a new three-way DNA junction-driven strand displacement mode and fabricated an aptamer-based label-free fluorescent sensing platform on the basis of this mechanism. Assembling the aptamer sequence into the three-way DNA junction makes the platform sensitive to the target of the aptamer. A label-free signal readout method, split G-quadruplex enhanced fluorescence of protoporphyrin IX (PPIX), was used to report the final signal. Here, adenosine triphosphatase (ATP) was taken as a model and detected through this approach, and DNA strand could also be detected by it. The mechanism was investigated by native polyacrylamide gel electrophoresis. Furthermore, on the basis of this molecular platform, we built a logic circuit with ATP and DNA strands as input. Aptamer played an important role in mediating the small molecule ATP to tune the DNA logic gate. Through altering the aptamer sequence, this molecular platform will be sensitive to various stimuli and applied in a wide field

Portable, Universal, and Visual Ion Sensing Platform Based on the Light Emitting Diode-Based Self-Referencing-Ion Selective Field-Effect Transistor

In this work, a novel and universal ion sensing platform was presented, which enables the visual detection of various ions with high sensitivity and selectivity. Coaxial potential signals (millivolt-scale) of the sample from the self-referencing (SR) ion selective chip can be transferred into the ad620-based amplifier with an output of volt-scale potentials. The amplified voltage is high enough to drive a light emitting diode (LED), which can be used as an amplifier and indicator to report the sample information. With this double amplification device (light emitting diode-based self-referencing-ion selective field-effect transistor, LED-SR-ISFET), a tiny change of the sample concentration can be observed with a distinguishable variation of LED brightness by visual inspection. This LED-based luminescent platform provided a facile, low-cost, and rapid sensing strategy without the need of additional expensive chemiluminescence reagent and instruments. Moreover, the SR mode also endows this device excellent stability and reliability. With this innovative design, sensitive determination of K⁺, H⁺, and Cl^– by the naked eye was achieved. It should also be noticed that this sensing strategy can easily be extended to other ions (or molecules) by simply integrating the corresponding ion (or molecule) selective electrode

Photoinduced Electron Transfer of DNA/Ag Nanoclusters Modulated by G‑Quadruplex/Hemin Complex for the Construction of Versatile Biosensors

Photoinduced electron transfer (PET) has been observed for the first time between DNA/Ag fluorescent nanoclusters (NCs) and G-quadruplex/hemin complexes, accompanied by a decrease in the fluorescence of the DNA/Ag NCs. In this PET process, a parallel G-quadruplex and the sensing sequences are blocked by a duplex. The specific combination of targets with the sensing sequence triggers the release of the G-quadruplex and allows it to fold properly and bind hemin to form a stable G-quadruplex/hemin complex. The complex proves favorable for PET because it makes the G-quadruplex bind hemin tightly, which promotes the electron transfer from the DNA/Ag NCs to the hemin Fe^III center, thus resulting in a decrease in the fluorescence intensity of the DNA/Ag NCs. This novel PET system enables the specific and versatile detection of target biomolecules such as DNA and ATP with high sensitivity based on the choices of different target sequences

Revealing the Molecular Structural Transformation of Hardwood and Softwood in Dilute Acid Flowthrough Pretreatment

To understand better the intrinsic recalcitrance of lignocellulosic biomass, the main hurdle to its efficient deconstruction, the effects of dilute acid flowthrough pretreatment on the dissolution chemistry of hemicellulose, cellulose, and lignin for both hardwood (e.g., poplar wood) and softwood (e.g., lodgepole pine wood) were investigated at temperatures of 200 to 270 °C and a flow rate of 25 mL/min with 0.05% (w/w) H₂SO₄. Results suggested that the softwood cellulose was more readily degraded into monomeric sugars than that of hardwood under same pretreatment conditions. However, while the hardwood lignin was completely removed into hydrolysate, ∼30% of the softwood lignin remained as solid residues under identical conditions, which was plausibly caused by vigorous C5-active recondensation reactions (C–C5). Effects of molecular structural features (i.e., lignin molecular weight, cellulose crystallinity, and condensed lignin structures) on the recalcitrance of hardwood and softwood to dilute acid pretreatment were identified for the first time in this study, providing important insights to establish the effective biomass pretreatment

G‑quadruplex-Based Fluorescent Assay of S1 Nuclease Activity and K⁺

Endonuclease plays an important role in many biological processes, and an assay of endonuclease activity is of great significance. However, traditional methods for the assay of endonuclease activity have undesirable limitations, such as high cost, DNA-consuming and laboriousness. In the present work, a G-quadruplex-based, fluorescent assay of endonuclease activity has been developed with protoporphyrin IX (PPIX) as a signal reporter. S1 nuclease, a single strand DNA (ssDNA)-specific endonuclease, is employed as model system. In the “on” state, G-quadruplex DNA can greatly enhance the fluorescence of PPIX. However, if S1 nuclease could cleave G-quadruplex DNA into small fragments, there would be no formation of G-quadruplexes, accompanied by low emission response of PPIX. This fluorescent discrimination before or after digestion by nuclease can be used to monitor the activity of S1 nuclease. This assay is simple in design and offers a convenient protocol for homogeneous, rapid and high-throughput detection. In addition, the proposed strategy avoids complicated covalent modifications or chemical labeling, and thus offers advantages of simplicity and cost efficiency. More importantly, K⁺ is found to well inhibit the activity of S1 nuclease when using certain G-quadruplex DNA as substrate, and thus this system is further used for turn-on detection of K⁺. S1 nuclease is critical in the detection of K⁺ since it helps to reduce the background signal

Mn²⁺ and Sb³⁺ Codoped Cs₂ZnCl₄ Metal Halide with Excitation-Wavelength-Dependent Emission for Fluorescence Anticounterfeiting

In recent years, there has been a growing demand for luminescence anticounterfeiting materials that possess the properties of environmentally friendly, single-component, and multimode fluorescence. Among the materials explored, the low dimensional metal halides have gained wide attention because of unique characteristics including low toxicity, simple synthesis, good stability, and so on. Here, we synthesized Mn2+ and Sb3+ codoped Cs2ZnCl4 single crystals by a facile hydrothermal method. Under 365 nm excitation, the codoped compound exhibits dual-band emissions at 530 and 730 nm. However, under 316 nm excitation, the compound only shows one emission band from 500 to 850 nm peaking at 730 nm, while under 460 nm excitation, the emission from 500 to 650 nm with an emission peak at 530 nm can be observed. Based on the study of the photoluminescence mechanism, the green and red emissions originate from the Mn2+ located in the tetrahedron and self-trapped exciton emission of [SbCl4]− clusters, respectively. Due to the zero-dimensional structure of the Cs2ZnCl4 host, there is minimal energy transfer between these dopants. Consequently, the luminous ratios of the two emissions can be independently regulated. Except by tuning the dopant concentrations, the Cs2ZnCl4:Mn2+, Sb3+ demonstrates excitation-wavelength-dependent properties, which could emit more than two colors with the change of excitation wavelength. As a result, multimode anticounterfeiting based on Cs2ZnCl4:Mn2+, Sb3+ crystals has been designed, which aligns with the requirements of environmentally friendly, single-component, and multimode fluorescence properties